The spaces are necessary, because the input is token based.
The program will read the second token in the file as a long integer
and use it as an identifier for the file. Thus, each file should
have a unique identifier following the pound symbol.

The -filetype map.inp tells the QTL Cartographer programs that this
is a map.inp formatted file. The bychromosome word is a vestige of
an idea that simply needs to hang around.